pdbHighlight 1.1.7 beta (tar/gz)

Release notes:

PDBHighlight: A Rasmol script database. Introduction The ultimate aim of pdbHighlight is to maintain a searchable database of Rasmol script files designed to highlight various features of the protein molecules whose structures are in the Protein Data Bank (PDB [1]). Currently the only scripts available are for highlighting PDB files according to the domain definitions of the Structural Classification of Proteins (SCOP [2]) database. Using pdbHighlight The ras_script utility is called with the following syntax ras_script < pdb-code > It calls the scopHighlight_using_flat_file.plx perl script which dumps a RasMol script to highlight the PDB file according to its SCOP domain annotation. ras_script creates a temporary file which combines the PDB file with the script file, and then invokes RasMol over this file. The scopHighlight_using_flat_file.plx script requires the SCOP parsable files [3] which can be downloaded using the wget_domain_data.plx utility script. Please check http://scop.mrc-lmb.cam.ac.uk/scop/index.html for the latest version of the data. All three perl scripts require various configuration options which should be obvious. All three could be improved by making this more obvious References [1] Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542 [2] Murzin AG, Brenner SE, Hubbard T, Chothia C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540 http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf [3] Lo Conte L, Brenner SE, Hubbard TJP, Chothia C, Murzin A. (2002). SCOP database in 2002: refinements accommodate structural genomics. Nucl. Acid Res. 30, 264-267 http://scop.mrc-lmb.cam.ac.uk/scop/ref/nar2002.pdf

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Changelog:

For a list of changes, please be patient :)